Merge pull request #716 from sanger/develop

Merging develop to master
sanger · Jan 17, 2025 · 39d58f3 · 39d58f3
2 parents 9444327 + efee450
commit 39d58f3
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diff --git a/.release-version b/.release-version
@@ -1 +1 @@
-1.23.0
+1.24.0
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -7,25 +7,25 @@ GIT
 GEM
   remote: https://rubygems.org/
   specs:
-    actionpack (7.0.8.5)
-      actionview (= 7.0.8.5)
-      activesupport (= 7.0.8.5)
+    actionpack (7.0.8.7)
+      actionview (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
       rack (~> 2.0, >= 2.2.4)
       rack-test (>= 0.6.3)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.0, >= 1.2.0)
-    actionview (7.0.8.5)
-      activesupport (= 7.0.8.5)
+    actionview (7.0.8.7)
+      activesupport (= 7.0.8.7)
       builder (~> 3.1)
       erubi (~> 1.4)
       rails-dom-testing (~> 2.0)
       rails-html-sanitizer (~> 1.1, >= 1.2.0)
-    activemodel (7.0.8.5)
-      activesupport (= 7.0.8.5)
-    activerecord (7.0.8.5)
-      activemodel (= 7.0.8.5)
-      activesupport (= 7.0.8.5)
-    activesupport (7.0.8.5)
+    activemodel (7.0.8.7)
+      activesupport (= 7.0.8.7)
+    activerecord (7.0.8.7)
+      activemodel (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
+    activesupport (7.0.8.7)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 1.6, < 2)
       minitest (>= 5.1)
@@ -44,7 +44,7 @@ GEM
     crass (1.0.6)
     diff-lcs (1.5.1)
     docile (1.4.0)
-    erubi (1.13.0)
+    erubi (1.13.1)
     factory_bot (6.5.0)
       activesupport (>= 5.0.0)
     factory_bot_rails (6.4.4)
@@ -73,23 +73,23 @@ GEM
     hashie (5.0.0)
     i18n (1.14.6)
       concurrent-ruby (~> 1.0)
-    json (2.8.2)
+    json (2.9.1)
     language_server-protocol (3.17.0.3)
     listen (3.9.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
-    loofah (2.23.1)
+    loofah (2.24.0)
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
     lumberjack (1.2.10)
     method_source (1.1.0)
     mini_portile2 (2.8.8)
-    minitest (5.25.2)
+    minitest (5.25.4)
     msgpack (1.7.2)
     multi_json (1.15.0)
     mysql2 (0.5.6)
     nenv (0.3.0)
-    nokogiri (1.16.7)
+    nokogiri (1.18.1)
       mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
     notiffany (0.1.3)
@@ -99,23 +99,23 @@ GEM
     parser (3.3.6.0)
       ast (~> 2.4.1)
       racc
-    pry (0.15.0)
+    pry (0.15.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
     racc (1.8.1)
     rack (2.2.10)
-    rack-test (2.1.0)
+    rack-test (2.2.0)
       rack (>= 1.3)
     rails-dom-testing (2.2.0)
       activesupport (>= 5.0.0)
       minitest
       nokogiri (>= 1.6)
-    rails-html-sanitizer (1.6.0)
+    rails-html-sanitizer (1.6.2)
       loofah (~> 2.21)
-      nokogiri (~> 1.14)
-    railties (7.0.8.5)
-      actionpack (= 7.0.8.5)
-      activesupport (= 7.0.8.5)
+      nokogiri (>= 1.15.7, != 1.16.7, != 1.16.6, != 1.16.5, != 1.16.4, != 1.16.3, != 1.16.2, != 1.16.1, != 1.16.0.rc1, != 1.16.0)
+    railties (7.0.8.7)
+      actionpack (= 7.0.8.7)
+      activesupport (= 7.0.8.7)
       method_source
       rake (>= 12.2)
       thor (~> 1.0)
@@ -126,7 +126,7 @@ GEM
     rb-inotify (0.11.1)
       ffi (~> 1.0)
     rbtree (0.4.6)
-    regexp_parser (2.9.2)
+    regexp_parser (2.10.0)
     rspec (3.13.0)
       rspec-core (~> 3.13.0)
       rspec-expectations (~> 3.13.0)
@@ -148,22 +148,22 @@ GEM
       rspec-mocks (~> 3.13)
       rspec-support (~> 3.13)
     rspec-support (3.13.1)
-    rubocop (1.68.0)
+    rubocop (1.69.2)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
       parser (>= 3.3.0.2)
       rainbow (>= 2.2.2, < 4.0)
-      regexp_parser (>= 2.4, < 3.0)
-      rubocop-ast (>= 1.32.2, < 2.0)
+      regexp_parser (>= 2.9.3, < 3.0)
+      rubocop-ast (>= 1.36.2, < 2.0)
       ruby-progressbar (~> 1.7)
-      unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.36.1)
+      unicode-display_width (>= 2.4.0, < 4.0)
+    rubocop-ast (1.37.0)
       parser (>= 3.3.1.0)
-    rubocop-performance (1.23.0)
+    rubocop-performance (1.23.1)
       rubocop (>= 1.48.1, < 2.0)
       rubocop-ast (>= 1.31.1, < 2.0)
-    rubocop-rails (2.27.0)
+    rubocop-rails (2.28.0)
       activesupport (>= 4.2.0)
       rack (>= 1.1)
       rubocop (>= 1.52.0, < 2.0)
@@ -190,7 +190,9 @@ GEM
     thor (1.3.2)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
-    unicode-display_width (2.6.0)
+    unicode-display_width (3.1.3)
+      unicode-emoji (~> 4.0, >= 4.0.4)
+    unicode-emoji (4.0.4)
     zeitwerk (2.7.1)
 
 PLATFORMS

diff --git a/app/models/aliquot.rb b/app/models/aliquot.rb
@@ -4,7 +4,7 @@
 # This model is used to store aliquot data
 class Aliquot < ApplicationRecord
   include ResourceTools
-  include SingularResourceTools
+  include SingularResourceVersionedTools
 
   def self.base_resource_key
     'aliquot_uuid'

diff --git a/db/migrate/20241211144506_add_hu_m_fre_code_to_sample.rb b/db/migrate/20241211144506_add_hu_m_fre_code_to_sample.rb
@@ -0,0 +1,5 @@
+class AddHuMFreCodeToSample < ActiveRecord::Migration[7.0]
+  def change
+    add_column :sample, :huMFre_code, :string, limit: 16
+  end
+end
diff --git a/db/schema.rb b/db/schema.rb
@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema[7.0].define(version: 2024_12_03_134455) do
+ActiveRecord::Schema[7.0].define(version: 2024_12_11_144506) do
   create_table "aliquot", charset: "utf8mb3", collation: "utf8mb3_unicode_ci", force: :cascade do |t|
     t.string "id_lims", null: false, comment: "The LIMS system that the aliquot was created in"
     t.string "aliquot_uuid", null: false, comment: "The UUID of the aliquot in the LIMS system"
@@ -366,6 +366,7 @@
     t.string "gc_content"
     t.string "dna_source"
     t.string "priority_level", comment: "Priority level eg Medium, High etc"
+    t.string "huMFre_code", limit: 16
     t.index ["accession_number"], name: "sample_accession_number_index"
     t.index ["id_lims", "id_sample_lims"], name: "index_sample_on_id_lims_and_id_sample_lims", unique: true
     t.index ["id_lims"], name: "index_sample_on_id_lims"

diff --git a/lib/singular_resource_versioned_tools.rb b/lib/singular_resource_versioned_tools.rb
@@ -0,0 +1,51 @@
+# frozen_string_literal: true
+
+# This module is used to store the latest version of a record and manage versioned records.
+# It provides methods to check if a record is the latest and if any attributes have changed,
+# and to create or update records accordingly. This ensures an audit trail of updates by
+# creating new records when necessary.
+module SingularResourceVersionedTools
+  extend ActiveSupport::Concern
+
+  EXCLUDED_ATTRIBUTES = %w[id created_at updated_at last_updated recorded_at].freeze
+
+  # Checks if the attributes of the given record have changed and if the given record is more recent.
+  # If both conditions are met, returns true. Otherwise, returns false.
+  #
+  # @param other [ActiveRecord::Base] The record to compare with.
+  # @return [Boolean] Returns true if the given record is the latest and has changed, false otherwise.
+  #
+  # Note: This method is used to ensure that only the most recent and changed records are processed,
+  # maintaining an audit trail of updates.
+  def latest?(other)
+    attributes_changed?(other) && (other.last_updated > last_updated)
+  end
+
+  # Compares the attributes of the current record with the given record, excluding 'id', 'created_at', and 'updated_at'.
+  #
+  # @param other [ActiveRecord::Base] The record to compare with.
+  # @return [Boolean] Returns true if the attributes have changed, false otherwise.
+  def attributes_changed?(other)
+    attributes.except(*EXCLUDED_ATTRIBUTES) != other.attributes.except(*EXCLUDED_ATTRIBUTES)
+  end
+
+  # This module is used to create or update a record
+  module ClassMethods
+    # Creates a record based on the given attributes.
+    # If an existing record with the same base resource key is found, it checks if the new record is the latest
+    # and if any attributes have changed. If both conditions are met, it creates a new record to maintain an audit trail.
+    #
+    # @param attributes [Hash] The attributes of the record to create or update which is an instance of Aliquot::JsonHandler.
+    # @return [ActiveRecord::Base] Returns the created record.
+    def create_or_update(attributes)
+      new_record = new(attributes.to_hash)
+
+      existing_record = for_lims(attributes.id_lims).with_id(attributes[base_resource_key]).order(last_updated: :desc)
+                                                    .first
+      return unless existing_record.nil? || existing_record.latest?(new_record)
+
+      create!(attributes.to_hash)
+    end
+    private :create_or_update
+  end
+end
diff --git a/spec/models/aliquot_spec.rb b/spec/models/aliquot_spec.rb
@@ -3,26 +3,30 @@
 require 'spec_helper'
 
 describe Aliquot do
-  context 'aliquot' do
-    let(:example_lims) { 'example' }
+  let(:example_lims) { 'example' }
+  let(:attribute_to_change) { 'volume' }
+  let(:new_value) { 10.0 }
 
-    let(:json) do
-      { 'id_lims' => 'example',
-        'aliquot_type' => 'DNA',
-        'volume' => 5.43,
-        'concentration' => 2.34,
-        'insert_size' => 100,
-        'aliquot_uuid' => '000000-0000-0000-0000-0000000002',
-        'source_type' => 'library',
-        'source_barcode' => 'PR-rna-00000001_H12',
-        'sample_name' => 'aliquot-sample',
-        'used_by_type' => 'pool',
-        'used_by_barcode' => 'pool-barcode',
-        'last_updated' => '2012-03-11 10:20:08',
-        'recorded_at' => '2012-03-11 10:20:08',
-        'created_at' => '2012-03-11 10:20:08' }
-    end
+  let(:json) do
+    { 'id_lims' => 'example',
+      'aliquot_type' => 'DNA',
+      'volume' => 5.43,
+      'concentration' => 2.34,
+      'insert_size' => 100,
+      'aliquot_uuid' => '000000-0000-0000-0000-0000000002',
+      'source_type' => 'library',
+      'source_barcode' => 'PR-rna-00000001_H12',
+      'sample_name' => 'aliquot-sample',
+      'used_by_type' => 'pool',
+      'used_by_barcode' => 'pool-barcode',
+      'last_updated' => '2012-03-11 10:20:08',
+      'recorded_at' => '2012-03-11 10:20:08',
+      'created_at' => '2012-03-11 10:20:08' }
+  end
 
+  it_behaves_like 'a singular resource versioned'
+
+  context 'aliquot' do
     it 'saves the correct resource' do
       expect(described_class.create_or_update_from_json(json, example_lims)).to be_truthy
     end